| AAString |
AAString objects |
| AAString-class |
AAString objects |
| AAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| AAStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| AA_ALPHABET |
AAString objects |
| ACtree |
PDict objects |
| ACtree-class |
PDict objects |
| ACtree2 |
PDict objects |
| ACtree2-class |
PDict objects |
| adjacentViews |
Basic functions for creating or modifying XStringViews objects |
| align-utils |
Utility functions related to sequence alignment |
| aligned |
AlignedXStringSet and QualityAlignedXStringSet objects |
| aligned,AlignedXStringSet0-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
| aligned,PairwiseAlignedFixedSubject-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
| AlignedXStringSet-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
| AlignedXStringSet0 |
AlignedXStringSet and QualityAlignedXStringSet objects |
| AlignedXStringSet0-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
| alignScore |
(Deprecated) Needleman-Wunsch Global Alignment |
| alignScore.needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
| alphabet |
BString objects |
| alphabet,ANY-method |
BString objects |
| alphabetFrequency |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,DNAString-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,DNAStringSet-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,MaskedXString-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,RNAString-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,RNAStringSet-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,XString-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,XStringSet-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency,XStringViews-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| AMINO_ACID_CODE |
The Single-Letter Amino Acid Code |
| append,QualityScaledXStringSet,QualityScaledXStringSet-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| append,XStringSet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| as.character,AlignedXStringSet0-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
| as.character,MaskedXString-method |
MaskedXString objects |
| as.character,PairwiseAlignedFixedSubject-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| as.character,XString-method |
BString objects |
| as.character,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| as.character,XStringViews-method |
The XStringViews class |
| as.complex,DNAString-method |
Turning a DNA sequence into a vector of complex numbers |
| as.integer,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| as.integer,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| as.list,MTB_PDict-method |
PDict objects |
| as.matrix,ACtree-method |
PDict objects |
| as.matrix,PairwiseAlignedFixedSubject-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| as.matrix,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| as.matrix,XStringViews-method |
The XStringViews class |
| as.numeric,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| as.numeric,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| cDNA |
DNA/RNA transcription and translation |
| CharacterToFASTArecords |
Read/write an XStringSet or XStringViews object from/to a file |
| chartr,ANY,ANY,MaskedXString-method |
Translating letters of a sequence |
| chartr,ANY,ANY,XString-method |
Translating letters of a sequence |
| chartr,ANY,ANY,XStringSet-method |
Translating letters of a sequence |
| chartr,ANY,ANY,XStringViews-method |
Translating letters of a sequence |
| class:AAString |
AAString objects |
| class:AAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| class:ACtree |
PDict objects |
| class:ACtree2 |
PDict objects |
| class:AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
| class:AlignedXStringSet0 |
AlignedXStringSet and QualityAlignedXStringSet objects |
| class:BOC2_SubjectString |
BOC\_SubjectString and BOC2\_SubjectString objects |
| class:BOC_SubjectString |
BOC\_SubjectString and BOC2\_SubjectString objects |
| class:BString |
BString objects |
| class:BStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| class:ByPos_MIndex |
MIndex objects |
| class:DNAString |
DNAString objects |
| class:DNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| class:InDel |
InDel objects |
| class:MaskedAAString |
MaskedXString objects |
| class:MaskedBString |
MaskedXString objects |
| class:MaskedDNAString |
MaskedXString objects |
| class:MaskedRNAString |
MaskedXString objects |
| class:MaskedXString |
MaskedXString objects |
| class:MIndex |
MIndex objects |
| class:MTB_PDict |
PDict objects |
| class:PairwiseAlignedFixedSubject |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| class:PairwiseAlignedFixedSubjectSummary |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| class:PairwiseAlignedXStringSet |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| class:PDict |
PDict objects |
| class:PDict3Parts |
PDict objects |
| class:PhredQuality |
PhredQuality and SolexaQuality objects |
| class:PreprocessedTB |
PDict objects |
| class:QualityAlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
| class:QualityScaledAAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledBStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledDNAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledRNAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledXStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:RNAString |
RNAString objects |
| class:RNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| class:SolexaQuality |
PhredQuality and SolexaQuality objects |
| class:TB_PDict |
PDict objects |
| class:Twobit |
PDict objects |
| class:XString |
BString objects |
| class:XStringPartialMatches |
XStringPartialMatches objects |
| class:XStringQuality |
PhredQuality and SolexaQuality objects |
| class:XStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| class:XStringViews |
The XStringViews class |
| codons |
DNA/RNA transcription and translation |
| codons,DNAString-method |
DNA/RNA transcription and translation |
| codons,MaskedDNAString-method |
DNA/RNA transcription and translation |
| codons,MaskedRNAString-method |
DNA/RNA transcription and translation |
| codons,RNAString-method |
DNA/RNA transcription and translation |
| coerce,AAString,MaskedAAString-method |
MaskedXString objects |
| coerce,BString,MaskedBString-method |
MaskedXString objects |
| coerce,BString,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,BString,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,BStringSet,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,BStringSet,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,character,AAString-method |
BString objects |
| coerce,character,AAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,character,BString-method |
BString objects |
| coerce,character,BStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,character,DNAString-method |
BString objects |
| coerce,character,DNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,character,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,character,RNAString-method |
BString objects |
| coerce,character,RNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,character,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,character,XString-method |
BString objects |
| coerce,character,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,DNAString,MaskedDNAString-method |
MaskedXString objects |
| coerce,integer,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,integer,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,MaskedAAString,AAString-method |
MaskedXString objects |
| coerce,MaskedBString,BString-method |
MaskedXString objects |
| coerce,MaskedDNAString,DNAString-method |
MaskedXString objects |
| coerce,MaskedRNAString,RNAString-method |
MaskedXString objects |
| coerce,MaskedXString,MaskCollection-method |
MaskedXString objects |
| coerce,MaskedXString,MaskedAAString-method |
MaskedXString objects |
| coerce,MaskedXString,MaskedBString-method |
MaskedXString objects |
| coerce,MaskedXString,MaskedDNAString-method |
MaskedXString objects |
| coerce,MaskedXString,MaskedRNAString-method |
MaskedXString objects |
| coerce,MaskedXString,NormalIRanges-method |
MaskedXString objects |
| coerce,MaskedXString,Views-method |
MaskedXString objects |
| coerce,MaskedXString,XStringViews-method |
MaskedXString objects |
| coerce,numeric,PhredQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,numeric,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
| coerce,PhredQuality,integer-method |
PhredQuality and SolexaQuality objects |
| coerce,PhredQuality,numeric-method |
PhredQuality and SolexaQuality objects |
| coerce,RNAString,MaskedRNAString-method |
MaskedXString objects |
| coerce,SolexaQuality,integer-method |
PhredQuality and SolexaQuality objects |
| coerce,SolexaQuality,numeric-method |
PhredQuality and SolexaQuality objects |
| coerce,XString,AAString-method |
BString objects |
| coerce,XString,AAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XString,BString-method |
BString objects |
| coerce,XString,BStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XString,DNAString-method |
BString objects |
| coerce,XString,DNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XString,RNAString-method |
BString objects |
| coerce,XString,RNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XString,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XStringSet,AAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XStringSet,BStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XStringSet,DNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XStringSet,RNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| coerce,XStringViews,AAStringSet-method |
The XStringViews class |
| coerce,XStringViews,BStringSet-method |
The XStringViews class |
| coerce,XStringViews,DNAStringSet-method |
The XStringViews class |
| coerce,XStringViews,RNAStringSet-method |
The XStringViews class |
| coerce,XStringViews,XStringSet-method |
The XStringViews class |
| compareStrings |
Utility functions related to sequence alignment |
| compareStrings,AlignedXStringSet0,AlignedXStringSet0-method |
Utility functions related to sequence alignment |
| compareStrings,character,character-method |
Utility functions related to sequence alignment |
| compareStrings,PairwiseAlignedXStringSet,missing-method |
Utility functions related to sequence alignment |
| compareStrings,XString,XString-method |
Utility functions related to sequence alignment |
| compareStrings,XStringSet,XStringSet-method |
Utility functions related to sequence alignment |
| complement |
Sequence reversing and complementing |
| complement,DNAString-method |
Sequence reversing and complementing |
| complement,DNAStringSet-method |
Sequence reversing and complementing |
| complement,MaskedDNAString-method |
Sequence reversing and complementing |
| complement,MaskedRNAString-method |
Sequence reversing and complementing |
| complement,RNAString-method |
Sequence reversing and complementing |
| complement,RNAStringSet-method |
Sequence reversing and complementing |
| complement,XStringViews-method |
Sequence reversing and complementing |
| complementedPalindromeArmLength |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeArmLength,DNAString-method |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeArmLength,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeLeftArm |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeLeftArm,DNAString-method |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeLeftArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeRightArm |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeRightArm,DNAString-method |
Searching a sequence for palindromes or complemented palindromes |
| complementedPalindromeRightArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
| complementSeq |
Complementary sequence. |
| consensusMatrix |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusMatrix,character-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusMatrix,list-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusMatrix,matrix-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusMatrix,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
| consensusMatrix,XStringSet-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusMatrix,XStringViews-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString,ANY-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString,matrix-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString,XStringSet-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString,XStringViews-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consmat |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consmat,ANY-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| countbases |
Obtain the ATCG content of a gene |
| countIndex |
MIndex objects |
| countIndex,ByPos_MIndex-method |
MIndex objects |
| countIndex,MIndex-method |
MIndex objects |
| countPattern |
String searching functions |
| countPattern,BOC2_SubjectString-method |
BOC\_SubjectString and BOC2\_SubjectString objects |
| countPattern,character-method |
String searching functions |
| countPattern,MaskedXString-method |
String searching functions |
| countPattern,XString-method |
String searching functions |
| countPattern,XStringSet-method |
String searching functions |
| countPattern,XStringViews-method |
String searching functions |
| countPDict |
Searching a sequence for patterns stored in a preprocessed dictionary |
| countPDict,MaskedXString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| countPDict,XString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| countPDict,XStringSet-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| countPDict,XStringViews-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| countPWM |
A simple PWM matching function and related utilities |
| coverage,AlignedXStringSet0-method |
Utility functions related to sequence alignment |
| coverage,MaskedXString-method |
Utility functions related to pattern matching |
| coverage,MIndex-method |
Utility functions related to pattern matching |
| coverage,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
| coverage,PairwiseAlignedFixedSubjectSummary-method |
Utility functions related to sequence alignment |
| mask |
Masking by content (or by position) |
| MaskedAAString |
MaskedXString objects |
| MaskedAAString-class |
MaskedXString objects |
| MaskedBString |
MaskedXString objects |
| MaskedBString-class |
MaskedXString objects |
| MaskedDNAString |
MaskedXString objects |
| MaskedDNAString-class |
MaskedXString objects |
| maskedratio,MaskedXString-method |
MaskedXString objects |
| MaskedRNAString |
MaskedXString objects |
| MaskedRNAString-class |
MaskedXString objects |
| maskedwidth,MaskedXString-method |
MaskedXString objects |
| MaskedXString |
MaskedXString objects |
| MaskedXString-class |
MaskedXString objects |
| maskMotif |
Masking by content (or by position) |
| maskMotif,MaskedXString,character-method |
Masking by content (or by position) |
| maskMotif,MaskedXString,XString-method |
Masking by content (or by position) |
| maskMotif,XString,ANY-method |
Masking by content (or by position) |
| masks |
MaskedXString objects |
| masks,MaskedXString-method |
MaskedXString objects |
| masks,XString-method |
MaskedXString objects |
| masks<- |
MaskedXString objects |
| masks<-,MaskedXString,MaskCollection-method |
MaskedXString objects |
| masks<-,MaskedXString,NULL-method |
MaskedXString objects |
| masks<-,XString,ANY-method |
MaskedXString objects |
| masks<-,XString,NULL-method |
MaskedXString objects |
| match,character,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| match,XString,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| match,XStringSet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| match-utils |
Utility functions related to pattern matching |
| matchDNAPattern |
String searching functions |
| matchLRPatterns |
Find paired matches in a sequence |
| matchLRPatterns,MaskedXString-method |
Find paired matches in a sequence |
| matchLRPatterns,XString-method |
Find paired matches in a sequence |
| matchLRPatterns,XStringViews-method |
Find paired matches in a sequence |
| matchPattern |
String searching functions |
| matchPattern,BOC2_SubjectString-method |
BOC\_SubjectString and BOC2\_SubjectString objects |
| matchPattern,BOC_SubjectString-method |
BOC\_SubjectString and BOC2\_SubjectString objects |
| matchPattern,character-method |
String searching functions |
| matchPattern,MaskedXString-method |
String searching functions |
| matchPattern,XString-method |
String searching functions |
| matchPattern,XStringSet-method |
String searching functions |
| matchPattern,XStringViews-method |
String searching functions |
| matchPDict |
Searching a sequence for patterns stored in a preprocessed dictionary |
| matchPDict,MaskedXString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| matchPDict,XString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| matchPDict,XStringSet-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| matchPDict,XStringViews-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
| matchPDict-exact |
Searching a sequence for patterns stored in a preprocessed dictionary |
| matchPDict-inexact |
Inexact matching with matchPDict()/countPDict()/whichPDict() |
| matchProbePair |
Find "theoretical amplicons" mapped to a probe pair |
| matchProbePair,DNAString-method |
Find "theoretical amplicons" mapped to a probe pair |
| matchProbePair,MaskedDNAString-method |
Find "theoretical amplicons" mapped to a probe pair |
| matchProbePair,XStringViews-method |
Find "theoretical amplicons" mapped to a probe pair |
| matchprobes |
A function to match a query sequence to the sequences of a set of probes. |
| matchPWM |
A simple PWM matching function and related utilities |
| maxScore |
A simple PWM matching function and related utilities |
| maxWeights |
A simple PWM matching function and related utilities |
| mergeIUPACLetters |
The IUPAC Extended Genetic Alphabet |
| MIndex |
MIndex objects |
| MIndex-class |
MIndex objects |
| mismatch |
Utility functions related to pattern matching |
| mismatch,AlignedXStringSet0,missing-method |
Utility functions related to sequence alignment |
| mismatch,ANY,XStringViews-method |
Utility functions related to pattern matching |
| mismatchSummary |
Utility functions related to sequence alignment |
| mismatchSummary,AlignedXStringSet0-method |
Utility functions related to sequence alignment |
| mismatchSummary,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
| mismatchSummary,PairwiseAlignedFixedSubjectSummary-method |
Utility functions related to sequence alignment |
| mismatchSummary,QualityAlignedXStringSet-method |
Utility functions related to sequence alignment |
| mismatchTable |
Utility functions related to sequence alignment |
| mismatchTable,AlignedXStringSet0-method |
Utility functions related to sequence alignment |
| mismatchTable,PairwiseAlignedXStringSet-method |
Utility functions related to sequence alignment |
| mismatchTable,QualityAlignedXStringSet-method |
Utility functions related to sequence alignment |
| mkAllStrings |
Calculate the frequency of oligonucleotides in a DNA or RNA sequence, plus some related functions |
| MTB_PDict |
PDict objects |
| MTB_PDict-class |
PDict objects |
| names,MIndex-method |
MIndex objects |
| names,PDict-method |
PDict objects |
| names,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| names<-,MIndex-method |
MIndex objects |
| names<-,PDict-method |
PDict objects |
| names<-,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| narrow,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| narrow,QualityScaledXStringSet-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| narrow,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| nchar,AlignedXStringSet0-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
| nchar,MaskedXString-method |
MaskedXString objects |
| nchar,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| nchar,PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| nchar,XString-method |
BString objects |
| nchar,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| nchar,XStringViews-method |
The XStringViews class |
| nedit |
Utility functions related to sequence alignment |
| nedit,PairwiseAlignedFixedSubjectSummary-method |
Utility functions related to sequence alignment |
| nedit,PairwiseAlignedXStringSet-method |
Utility functions related to sequence alignment |
| neditAt |
Utility functions related to pattern matching |
| neditEndingAt |
Utility functions related to pattern matching |
| neditEndingAt,character-method |
Utility functions related to pattern matching |
| neditEndingAt,XString-method |
Utility functions related to pattern matching |
| neditEndingAt,XStringSet-method |
Utility functions related to pattern matching |
| neditStartingAt |
Utility functions related to pattern matching |
| neditStartingAt,character-method |
Utility functions related to pattern matching |
| neditStartingAt,XString-method |
Utility functions related to pattern matching |
| neditStartingAt,XStringSet-method |
Utility functions related to pattern matching |
| needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
| needwunsQS,character,character-method |
(Deprecated) Needleman-Wunsch Global Alignment |
| needwunsQS,character,XString-method |
(Deprecated) Needleman-Wunsch Global Alignment |
| needwunsQS,XString,character-method |
(Deprecated) Needleman-Wunsch Global Alignment |
| needwunsQS,XString,XString-method |
(Deprecated) Needleman-Wunsch Global Alignment |
| nindel |
AlignedXStringSet and QualityAlignedXStringSet objects |
| nindel,AlignedXStringSet0-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
| nindel,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| nindel,PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| nmatch |
Utility functions related to pattern matching |
| nmatch,ANY,XStringViews-method |
Utility functions related to pattern matching |
| nmatch,PairwiseAlignedFixedSubjectSummary,missing-method |
Utility functions related to sequence alignment |
| nmatch,PairwiseAlignedXStringSet,missing-method |
Utility functions related to sequence alignment |
| nmismatch |
Utility functions related to pattern matching |
| nmismatch,AlignedXStringSet0,missing-method |
Utility functions related to sequence alignment |
| nmismatch,ANY,XStringViews-method |
Utility functions related to pattern matching |
| nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method |
Utility functions related to sequence alignment |
| nmismatch,PairwiseAlignedXStringSet,missing-method |
Utility functions related to sequence alignment |
| nmismatchEndingAt |
Utility functions related to pattern matching |
| nmismatchStartingAt |
Utility functions related to pattern matching |
| nucleotideFrequencyAt |
Calculate the frequency of oligonucleotides in a DNA or RNA sequence, plus some related functions |
| nucleotideFrequencyAt,XStringSet-method |
Calculate the frequency of oligonucleotides in a DNA or RNA sequence, plus some related functions |
| nucleotideFrequencyAt,XStringViews-method |
Calculate the frequency of oligonucleotides in a DNA or RNA sequence, plus some related functions |
| nucleotideSubstitutionMatrix |
Scoring matrices |
| PairwiseAlignedFixedSubject |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubject,character,character-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubject,character,missing-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubject,XString,XString-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubject,XStringSet,missing-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubject-class |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubjectSummary |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedFixedSubjectSummary-class |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedXStringSet |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedXStringSet,character,character-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedXStringSet,character,missing-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedXStringSet,XString,XString-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedXStringSet,XStringSet,missing-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| PairwiseAlignedXStringSet-class |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| pairwiseAlignment |
Optimal Pairwise Alignment |
| pairwiseAlignment,character,character-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,character,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,character,XString-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,character,XStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,QualityScaledXStringSet,character-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,QualityScaledXStringSet,XString-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,QualityScaledXStringSet,XStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XString,character-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XString,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XString,XString-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XString,XStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XStringSet,character-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XStringSet,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XStringSet,XString-method |
Optimal Pairwise Alignment |
| pairwiseAlignment,XStringSet,XStringSet-method |
Optimal Pairwise Alignment |
| palindromeArmLength |
Searching a sequence for palindromes or complemented palindromes |
| palindromeArmLength,XString-method |
Searching a sequence for palindromes or complemented palindromes |
| palindromeArmLength,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
| palindromeLeftArm |
Searching a sequence for palindromes or complemented palindromes |
| palindromeLeftArm,XString-method |
Searching a sequence for palindromes or complemented palindromes |
| palindromeLeftArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
| palindromeRightArm |
Searching a sequence for palindromes or complemented palindromes |
| palindromeRightArm,XString-method |
Searching a sequence for palindromes or complemented palindromes |
| palindromeRightArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
| PAM120 |
Scoring matrices |
| PAM250 |
Scoring matrices |
| PAM30 |
Scoring matrices |
| PAM40 |
Scoring matrices |
| PAM70 |
Scoring matrices |
| pattern |
XStringPartialMatches objects |
| pattern,PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| pattern,XStringPartialMatches-method |
XStringPartialMatches objects |
| patternFrequency |
PDict objects |
| patternFrequency,PDict-method |
PDict objects |
| PDict |
PDict objects |
| PDict,AsIs-method |
PDict objects |
| PDict,character-method |
PDict objects |
| PDict,DNAStringSet-method |
PDict objects |
| PDict,XStringViews-method |
PDict objects |
| PDict-class |
PDict objects |
| PDict3Parts |
PDict objects |
| PDict3Parts-class |
PDict objects |
| phiX174Phage |
Versions of bacteriophage phiX174 complete genome and sample short reads |
| PhredQuality |
PhredQuality and SolexaQuality objects |
| PhredQuality-class |
PhredQuality and SolexaQuality objects |
| pid |
Percent Sequence Identity |
| pid,PairwiseAlignedXStringSet-method |
Percent Sequence Identity |
| pmatchPattern |
Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern,XStringViews-method |
Longest Common Prefix/Suffix/Substring searching functions |
| PreprocessedTB |
PDict objects |
| PreprocessedTB-class |
PDict objects |
| print.needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
| PWMscore |
A simple PWM matching function and related utilities |
| PWMscoreStartingAt |
A simple PWM matching function and related utilities |
| score,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| score,PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| setdiff,XStringSet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| setequal,XStringSet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| show,ACtree-method |
PDict objects |
| show,ACtree2-method |
PDict objects |
| show,AlignedXStringSet0-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
| show,ByPos_MIndex-method |
MIndex objects |
| show,MaskedXString-method |
MaskedXString objects |
| show,MTB_PDict-method |
PDict objects |
| show,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| show,PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| show,QualityScaledXStringSet-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| show,TB_PDict-method |
PDict objects |
| show,Twobit-method |
PDict objects |
| show,XString-method |
BString objects |
| show,XStringPartialMatches-method |
XStringPartialMatches objects |
| show,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| show,XStringViews-method |
The XStringViews class |
| SolexaQuality |
PhredQuality and SolexaQuality objects |
| SolexaQuality-class |
PhredQuality and SolexaQuality objects |
| sort,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| srPhiX174 |
Versions of bacteriophage phiX174 complete genome and sample short reads |
| start,AlignedXStringSet0-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
| startIndex |
MIndex objects |
| startIndex,ByPos_MIndex-method |
MIndex objects |
| stringDist |
String Distance/Alignment Score Matrix |
| stringDist,character-method |
String Distance/Alignment Score Matrix |
| stringDist,QualityScaledXStringSet-method |
String Distance/Alignment Score Matrix |
| stringDist,XStringSet-method |
String Distance/Alignment Score Matrix |
| strrev |
Sequence reversing and complementing |
| subBString |
Fast substring extraction |
| subject,PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
| subpatterns |
XStringPartialMatches objects |
| subpatterns,XStringPartialMatches-method |
XStringPartialMatches objects |
| subseq,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| subseq,MaskedXString-method |
MaskedXString objects |
| subseq,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| subseq<-,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| subseq<-,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
| substitution.matrices |
Scoring matrices |
| substr,MaskedXString-method |
Fast substring extraction |
| substr,XString-method |
Fast substring extraction |
| substring,MaskedXString-method |
Fast substring extraction |
| substring,XString-method |
Fast substring extraction |
| subXString |
Fast substring extraction |
| summary,PairwiseAlignedFixedSubject-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |